Main
Evgeniia Chikina
I am a bioinformatician with a medical background. I use my medical and biological knowledge to combine with the world of computer science. At the moment, I have particularly good knowledge and skills in analyzing single cell RNA sequencing data.
Education
PhD Student, Cellular biology
Koltzov Institute of Developmental Biology of Russian Academy of Sciences
Moscow, Russia
Current - 2022
Master’s degree (with honors), Applied Mathematics and Informatics, Bioinformatics and System Biology
ITMO University
Saint-Petersburg, Russia
2022 - 2020
- Thesis: Metabolic Modules Identification in Single-Cell Data
- Course Project: Identifying Metabolic Modules in TCGA Datasets
- Semester Project: Effects of Background RNA Noise on Differential Expression Results in scRNA-seq
Specialist degree (with honors), Pediatrician
Saint-Petersburg State Pediatric Medical University
Saint-Petersburg, Russia
2020 - 2014
- Pediatrician
Research Projects
Metabolic Modules Identification in Single-Cell Data
ITMO University
Saint-Petersburg, Russia
2022 - 2021
- Thesis
- Main goal of the project is to extend applications of the GAM-clustering tool on the single-cell RNA-seq data. In order to find optimal clustering algorithm performed and analysed multiple clustering strategies for the single-cell RNA-seq data. Used trajectories and gene set enrichment analysis for biological interpretation of the results. Involved in the modification of the tool.
Identifying Metabolic Modules in TCGA Datasets
ITMO University
Saint-Petersburg, Russia
2021
- Course Project
- With previousy developed GAM-clustering algorithm analyzed TCGA datasets (LUSC) - bulk RNA-seq data. Identified metabolic modules and performed biological analysis of them. During work was involved in the modification of the tool and testing.
Effects of Background RNA Noise on Differential Expression Results in scRNA-seq
ITMO University
Saint-Petersburg, Russia
2020
- Performed standart analysis of the single-cell data with Seurat pipeline and integration of multiple samples using SCTransform intgration. With help of
DropletUtilsR package identified ambient RNA and tried to estimate the impact of it on the differential expression results.
Other Projects
vDiveR ShinyApp
Perdana University (Students Project)
N/A
Current - 2022
- DiveR is a graphical user interface (GUI)-based web application hosted on R Shiny for the visualization of DiMA results, a tool designed to facilitate the dissection of protein sequence diversity dynamics for viruses.
- Modifications of ShinyApp scripts
- https://github.com/pendy05/vDiveR_RShiny
Conferences
IMGC 2023
36th International Mammalian Genome Conference
Tsukuba, Japan (online)
2023
- Evgeniia Chikina, Anastasiia Gainullina, Elena Shagimardanova, Alexander Nesmelov, Airat Bilyalov, Oleg Gusev, Roman Romanov. Hypothalamic cell diversity underlying behavioral differences in the American mink (Neogale vison).
- The best virtual trainee poster
MCCMB’23
11th Moscow Conference on Computational Molecular Biology
Moscow, Russia
2023
- Evgeniia Chikina, Victoria Melnikova, Anastasiia Gainullina, Roman A. Romanov. Hypothalamic neurons in type I diabetes at a single-cell resolution. ISBN 978-5-901158-33-3
- Poster
Lomonosov 2023
30th International Scientific Conference for Undergraduate and Graduate Students and Young Scientists “Lomonosov”
Moscow, Russia
2023
- Evgeniia Chikina. Study of diabetes-specific hypothalamic changes at the single cell level. ISBN 978-5-317-06952-0
Anniversary Scientific Conference «Nikolay Konstantinovich Koltzov and the Biology of the XXI century»
Koltzov Institute of Developmental Biology of Russian Academy of Sciences
Moscow, Russia
2022
- Evgeniia Chikina, Anastasiia Gainullina, Roman A. Romanov. Metabolic modules of single cells of the hypothalamus in normal conditions and in metabolic disorders. ISBN 978-5-00204-554-9
- Poster
Nationwide scientific forum of students and young scientists with international participation «Student science – 2018»
Saint-Petersburg State Pediatric Medical University
Saint-Petersburg, Russia
2018
- Chikina E.A., Shtukina E.D. Study of microbiological landscape and microorganism susceptibility analysis to antibacterial drugs in the neonatal and premature infants intensive care department, cardiac intensive care department and neonatal pathology department for the period from 2014 to 2017.
- Pharmacology Section: 3d degree diploma
Publications
iPSC-Derived Macrophages: The Differentiation Protocol Affects Cell Immune Characteristics and Differentiation Trajectories.
Klepikova, A.; Nenasheva, T.; Sheveleva, O.; Protasova, E.; Antonov, D.; Gainullina, A.; Chikina, E.; Sakovnich, O.; Gerasimova, T.; Nikitina, I.; et al. Int. J. Mol. Sci. 2022, 23, 16087. https://doi.org/10.3390/ijms232416087
N/A
2022
Achievements
IMGC 2023: Best virtual trainee poster
36th International Mammalian Genome Conference
Tsukuba, Japan (online)
2023
Annual University Olympiad in Pediatrics
Saint-Petersburg State Pediatric Medical University
Saint-Petersburg, Russia
2018
- 1st degree diploma
University Olympiad in Propaedeutics of Children’s Diseases
Saint-Petersburg State Pediatric Medical University
Saint-Petersburg, Russia
2017
- 2nd degree diploma
Teaching experience
Chemistry/Biology School Tutor
N/A
Saint-Petersburg, Russia
2020 - 2018
- I was teaching 6-9th grade school students chemistry and biology to increase their knowledge in the field and in some cases helped studying for school exams.
Courses
Introduction to Probability and Data with R (en)
Duke University
Coursera, Online
2022
Molecular biology of the cell (ru)
Bioinformatics Institute
Stepik, Online
2020
Programming in Python (ru)
Bioinformatics Institute
Stepik, Online
2019